envs/01_qc.yml
set.seed(3980)
start_time <- Sys.time()
start_time
## [1] "2026-02-06 16:06:59 -05"
library(htmltools)
conda activate nanoplot
NanoPlot --version
NanoPlot 1.44.1
NanoPlot --fastq Data/prueba.fastq.gz --outdir Analysis/01_qc/nanoplot
cat(readLines("Analysis/01_qc/nanoplot_pre_qc/NanoStats.txt"), sep ="\n")
## General summary:
## Mean read length: 3,905.0
## Mean read quality: 8.4
## Median read length: 3,140.0
## Median read quality: 9.5
## Number of reads: 40,000.0
## Read length N50: 5,093.0
## STDEV read length: 3,269.0
## Total bases: 156,199,195.0
## Number, percentage and megabases of reads above quality cutoffs
## >Q10: 10460 (26.2%) 45.4Mb
## >Q15: 0 (0.0%) 0.0Mb
## >Q20: 0 (0.0%) 0.0Mb
## >Q25: 0 (0.0%) 0.0Mb
## >Q30: 0 (0.0%) 0.0Mb
## Top 5 highest mean basecall quality scores and their read lengths
## 1: 11.9 (258)
## 2: 11.7 (975)
## 3: 11.7 (3671)
## 4: 11.7 (2385)
## 5: 11.7 (1252)
## Top 5 longest reads and their mean basecall quality score
## 1: 40044 (9.7)
## 2: 35177 (8.1)
## 3: 34668 (9.7)
## 4: 34637 (10.5)
## 5: 33834 (9.5)
htmltools::includeHTML("Analysis/01_qc/nanoplot_pre_qc/Yield_By_Length.html")
htmltools::includeHTML("Analysis/01_qc/nanoplot_pre_qc/WeightedHistogramReadlength.html")
htmltools::includeHTML("Analysis/01_qc/nanoplot_pre_qc/LengthvsQualityScatterPlot_kde.html")
conda deactivate
conda activate filtlong
filtlong --version
Filtlong v0.2.1
filtlong --min_length 1000 --min_mean_q 7 prueba.fastq.gz | gzip > prueba.L1000.Q7.fastq.gz
conda deactivate
conda activate nanoplot
NanoPlot --version
NanoPlot 1.44.1
NanoPlot --fastq Data/prueba.L1000.Q7.fastq.gz --outdir Analysis/01_qc/nanoplotpostqc
cat(readLines("Analysis/01_qc/nanoplot_post_qc/NanoStats.txt"), sep ="\n")
## General summary:
## Mean read length: 4,276.8
## Mean read quality: 8.7
## Median read length: 3,424.0
## Median read quality: 9.5
## Number of reads: 35,977.0
## Read length N50: 5,155.0
## STDEV read length: 3,240.3
## Total bases: 153,867,890.0
## Number, percentage and megabases of reads above quality cutoffs
## >Q10: 10065 (28.0%) 45.1Mb
## >Q15: 0 (0.0%) 0.0Mb
## >Q20: 0 (0.0%) 0.0Mb
## >Q25: 0 (0.0%) 0.0Mb
## >Q30: 0 (0.0%) 0.0Mb
## Top 5 highest mean basecall quality scores and their read lengths
## 1: 11.7 (3671)
## 2: 11.7 (2385)
## 3: 11.7 (1252)
## 4: 11.6 (2680)
## 5: 11.6 (1854)
## Top 5 longest reads and their mean basecall quality score
## 1: 40044 (9.7)
## 2: 35177 (8.1)
## 3: 34668 (9.7)
## 4: 34637 (10.5)
## 5: 33834 (9.5)
htmltools::includeHTML("Analysis/01_qc/nanoplot_post_qc/Yield_By_Length.html")
htmltools::includeHTML("Analysis/01_qc/nanoplot_post_qc/WeightedHistogramReadlength.html")
htmltools::includeHTML("Analysis/01_qc/nanoplot_post_qc/LengthvsQualityScatterPlot_kde.html")